My biggest issue with the game's big meta-secret (major spoilers):
Where does the game teach you that the cross-lines mean a double press of the direction? That tripped me up for the longest time, and the only way I could break through that confusion was by looking it up in a guide.
I don't remember if it tells you in the manual, but the Holy Cross puzzle in the old house is very simple but features a cross bar— so if you figure it out there you are good to go.